Figure 3: Substrates and analogues bound to the PceA substrate-binding pocket.
From: Cobamide-mediated enzymatic reductive dehalogenation via long-range electron transfer
(a) Positioning of 2,4,6-TBP, 2,4-DBP and 4-BP. An overlay of the three substrates is depicted in the inset. Stereo representations are shown in Supplementary Fig. 3. (b) Positioning of the meta-halogenated 3-BP. (c) Influence of halogen type on positioning of para-halogenated phenols. In the direction shown, the binding site is flanked by Tyr382, Tyr102 and the corrin ring. For all substrates, 1 sigma 2Fo−Fc electron density (blue) for substrate, Co-ligand water/hydroxyl and the first water molecule in the substrate channel are shown. Anomalous difference density (indicative of a heavy atom) is shown around the substrate for bromine (5 sigma map, red stick), chlorine (3.5 sigma, green stick) or iodine (5 sigma, violet stick). The hydroxyl group is shown in black. (S) Indicates the leaving group of a substrate. Note that products were bound to PceA at high concentrations and represent substrate rather than product, except for a signal modelled as iodide ion which may have dissociated from 4-IP in the 1.9 Å wavelength X-ray beam. 2,4-DBP was incubated in a buffer containing 200 mM Cl−; other incubations were performed in chloride-free buffer. 2,4-DBP and 4-BP were incubated in the presence of 2 mM Ti(III) citrate and 0.2 mM methyl viologen. No cobalt β-ligand was modelled for 4-CP because of the lower resolution (2.3 Å versus 1.6–1.9 Å for other structures).
